Starting phenix.real_space_refine on Wed Mar 4 16:38:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vfl_21186/03_2026/6vfl_21186.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vfl_21186/03_2026/6vfl_21186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vfl_21186/03_2026/6vfl_21186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vfl_21186/03_2026/6vfl_21186.map" model { file = "/net/cci-nas-00/data/ceres_data/6vfl_21186/03_2026/6vfl_21186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vfl_21186/03_2026/6vfl_21186.cif" } resolution = 4.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 9306 2.51 5 N 2466 2.21 5 O 3054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14925 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3536 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 3 Chain: "B" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3536 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 3 Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "E" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3536 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 3 Chain: "F" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.47, per 1000 atoms: 0.23 Number of scatterers: 14925 At special positions: 0 Unit cell: (129.95, 125.35, 115, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 3054 8.00 N 2466 7.00 C 9306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.11 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.11 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.11 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA Q 3 " - " MAN Q 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA Q 3 " - " MAN Q 5 " " BMA a 3 " - " MAN a 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A 608 " - " ASN A 160 " " NAG A 609 " - " ASN A 276 " " NAG A 612 " - " ASN A 386 " " NAG A 613 " - " ASN A 363 " " NAG A 618 " - " ASN A 133 " " NAG A 627 " - " ASN A 289 " " NAG A 630 " - " ASN A 339 " " NAG A 631 " - " ASN A 355 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 608 " - " ASN C 160 " " NAG C 609 " - " ASN C 276 " " NAG C 612 " - " ASN C 386 " " NAG C 613 " - " ASN C 363 " " NAG C 618 " - " ASN C 133 " " NAG C 627 " - " ASN C 289 " " NAG C 630 " - " ASN C 339 " " NAG C 631 " - " ASN C 355 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 611 " " NAG E 608 " - " ASN E 160 " " NAG E 609 " - " ASN E 276 " " NAG E 612 " - " ASN E 386 " " NAG E 613 " - " ASN E 363 " " NAG E 618 " - " ASN E 133 " " NAG E 627 " - " ASN E 289 " " NAG E 630 " - " ASN E 339 " " NAG E 631 " - " ASN E 355 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN A 262 " " NAG H 1 " - " ASN A 448 " " NAG I 1 " - " ASN A 295 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 197 " " NAG L 1 " - " ASN A 156 " " NAG M 1 " - " ASN A 301 " " NAG N 1 " - " ASN A 88 " " NAG O 1 " - " ASN A 241 " " NAG P 1 " - " ASN A 332 " " NAG Q 1 " - " ASN C 262 " " NAG R 1 " - " ASN C 448 " " NAG S 1 " - " ASN C 295 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 197 " " NAG V 1 " - " ASN C 156 " " NAG W 1 " - " ASN C 301 " " NAG X 1 " - " ASN C 88 " " NAG Y 1 " - " ASN C 241 " " NAG Z 1 " - " ASN C 332 " " NAG a 1 " - " ASN E 262 " " NAG b 1 " - " ASN E 448 " " NAG c 1 " - " ASN E 295 " " NAG d 1 " - " ASN E 234 " " NAG e 1 " - " ASN E 197 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 301 " " NAG h 1 " - " ASN E 88 " " NAG i 1 " - " ASN E 241 " " NAG j 1 " - " ASN E 332 " Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 463.3 milliseconds 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3198 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 33 sheets defined 29.3% alpha, 51.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.228A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.930A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.113A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.919A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.830A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 544 No H-bonds generated for 'chain 'B' and resid 543 through 544' Processing helix chain 'B' and resid 545 through 549 Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.543A pdb=" N ILE B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 658 Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.228A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.928A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.113A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 removed outlier: 4.919A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.831A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 544 No H-bonds generated for 'chain 'D' and resid 543 through 544' Processing helix chain 'D' and resid 545 through 549 Processing helix chain 'D' and resid 569 through 596 removed outlier: 3.542A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 658 Processing helix chain 'E' and resid 61 through 66 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.227A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 334 through 354 removed outlier: 3.928A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.113A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.919A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.830A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 544 No H-bonds generated for 'chain 'F' and resid 543 through 544' Processing helix chain 'F' and resid 545 through 549 Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.543A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 658 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.601A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.706A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.515A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.771A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 4.080A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 316 through 323A removed outlier: 5.409A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.124A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.771A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.512A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.602A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.706A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.516A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.771A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 271 through 274 removed outlier: 4.081A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 316 through 323A removed outlier: 5.409A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.124A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.771A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 393 through 395 removed outlier: 6.512A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.601A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD1, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.705A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.515A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.825A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 271 through 274 removed outlier: 4.082A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 316 through 323A removed outlier: 5.408A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.124A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 10.825A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 393 through 395 removed outlier: 6.512A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1791 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3408 1.32 - 1.45: 4543 1.45 - 1.58: 7118 1.58 - 1.72: 3 1.72 - 1.85: 129 Bond restraints: 15201 Sorted by residual: bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.416 0.081 1.40e-02 5.10e+03 3.33e+01 bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.417 0.080 1.40e-02 5.10e+03 3.29e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.417 0.080 1.40e-02 5.10e+03 3.26e+01 bond pdb=" NE1 TRP C 479 " pdb=" CE2 TRP C 479 " ideal model delta sigma weight residual 1.370 1.320 0.050 1.10e-02 8.26e+03 2.05e+01 bond pdb=" NE1 TRP A 479 " pdb=" CE2 TRP A 479 " ideal model delta sigma weight residual 1.370 1.321 0.049 1.10e-02 8.26e+03 2.02e+01 ... (remaining 15196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 15903 1.78 - 3.56: 3692 3.56 - 5.34: 814 5.34 - 7.12: 192 7.12 - 8.90: 36 Bond angle restraints: 20637 Sorted by residual: angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 128.46 -8.90 1.01e+00 9.80e-01 7.77e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 128.46 -8.90 1.01e+00 9.80e-01 7.76e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 128.42 -8.86 1.01e+00 9.80e-01 7.70e+01 angle pdb=" N GLN A 258 " pdb=" CA GLN A 258 " pdb=" C GLN A 258 " ideal model delta sigma weight residual 111.36 118.69 -7.33 1.09e+00 8.42e-01 4.52e+01 angle pdb=" N GLN C 258 " pdb=" CA GLN C 258 " pdb=" C GLN C 258 " ideal model delta sigma weight residual 111.36 118.68 -7.32 1.09e+00 8.42e-01 4.51e+01 ... (remaining 20632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.58: 10030 21.58 - 43.15: 305 43.15 - 64.73: 66 64.73 - 86.30: 33 86.30 - 107.88: 12 Dihedral angle restraints: 10446 sinusoidal: 5508 harmonic: 4938 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -134.94 48.94 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -134.90 48.90 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -134.89 48.89 1 1.00e+01 1.00e-02 3.29e+01 ... (remaining 10443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2044 0.119 - 0.239: 545 0.239 - 0.358: 36 0.358 - 0.478: 0 0.478 - 0.597: 3 Chirality restraints: 2628 Sorted by residual: chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 chirality pdb=" C1 BMA Q 3 " pdb=" O4 NAG Q 2 " pdb=" C2 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.00e+02 chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.79e+01 ... (remaining 2625 not shown) Planarity restraints: 2547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 611 " -0.064 2.00e-02 2.50e+03 6.70e-02 5.62e+01 pdb=" CG ASN F 611 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN F 611 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN F 611 " 0.105 2.00e-02 2.50e+03 pdb=" C1 NAG F 703 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " -0.064 2.00e-02 2.50e+03 6.70e-02 5.60e+01 pdb=" CG ASN B 611 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " 0.105 2.00e-02 2.50e+03 pdb=" C1 NAG B 703 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 611 " -0.064 2.00e-02 2.50e+03 6.69e-02 5.59e+01 pdb=" CG ASN D 611 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN D 611 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN D 611 " 0.105 2.00e-02 2.50e+03 pdb=" C1 NAG D 703 " -0.080 2.00e-02 2.50e+03 ... (remaining 2544 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3526 2.78 - 3.31: 13398 3.31 - 3.84: 24752 3.84 - 4.37: 29411 4.37 - 4.90: 46903 Nonbonded interactions: 117990 Sorted by model distance: nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.248 3.040 nonbonded pdb=" N ASN C 355 " pdb=" OD1 ASN C 355 " model vdw 2.391 3.120 nonbonded pdb=" N ASN E 355 " pdb=" OD1 ASN E 355 " model vdw 2.391 3.120 ... (remaining 117985 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'a' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.410 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.113 15336 Z= 1.099 Angle : 1.717 8.904 21009 Z= 1.069 Chirality : 0.100 0.597 2628 Planarity : 0.009 0.039 2484 Dihedral : 11.834 107.876 7149 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.20 % Allowed : 0.39 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.19), residues: 1674 helix: -0.13 (0.24), residues: 420 sheet: 1.34 (0.22), residues: 411 loop : 0.79 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 192 TYR 0.068 0.008 TYR B 638 PHE 0.028 0.006 PHE A 383 TRP 0.050 0.010 TRP E 96 HIS 0.008 0.003 HIS B 585 Details of bonding type rmsd covalent geometry : bond 0.02027 (15201) covalent geometry : angle 1.69404 (20637) SS BOND : bond 0.02761 ( 33) SS BOND : angle 2.49081 ( 66) hydrogen bonds : bond 0.16540 ( 555) hydrogen bonds : angle 7.35106 ( 1791) link_ALPHA1-3 : bond 0.04000 ( 3) link_ALPHA1-3 : angle 3.54710 ( 9) link_ALPHA1-6 : bond 0.02879 ( 3) link_ALPHA1-6 : angle 3.07845 ( 9) link_BETA1-4 : bond 0.03337 ( 33) link_BETA1-4 : angle 3.05150 ( 99) link_NAG-ASN : bond 0.02802 ( 63) link_NAG-ASN : angle 2.48207 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 456 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8996 (m) cc_final: 0.8668 (p) REVERT: A 180 ASP cc_start: 0.8917 (m-30) cc_final: 0.8614 (m-30) REVERT: A 195 ASN cc_start: 0.9275 (p0) cc_final: 0.9020 (p0) REVERT: A 233 PHE cc_start: 0.9195 (t80) cc_final: 0.8700 (t80) REVERT: A 251 ILE cc_start: 0.9167 (mt) cc_final: 0.8800 (mm) REVERT: A 300 ASN cc_start: 0.8908 (m-40) cc_final: 0.7758 (p0) REVERT: A 342 LEU cc_start: 0.9621 (mt) cc_final: 0.9410 (mm) REVERT: B 530 MET cc_start: 0.8896 (mtp) cc_final: 0.8489 (mtp) REVERT: B 536 THR cc_start: 0.8683 (p) cc_final: 0.8121 (t) REVERT: B 540 GLN cc_start: 0.9170 (mp-120) cc_final: 0.8878 (mp10) REVERT: B 543 ASN cc_start: 0.8475 (m-40) cc_final: 0.7974 (t0) REVERT: B 591 GLN cc_start: 0.9328 (tt0) cc_final: 0.8873 (tt0) REVERT: B 615 SER cc_start: 0.8959 (t) cc_final: 0.8650 (m) REVERT: B 617 ARG cc_start: 0.7662 (ttm-80) cc_final: 0.7046 (mmm-85) REVERT: B 618 ASN cc_start: 0.6401 (m110) cc_final: 0.6177 (m110) REVERT: B 643 TYR cc_start: 0.8850 (m-10) cc_final: 0.8626 (m-10) REVERT: C 51 THR cc_start: 0.9008 (m) cc_final: 0.8627 (p) REVERT: C 180 ASP cc_start: 0.8995 (m-30) cc_final: 0.8769 (m-30) REVERT: C 195 ASN cc_start: 0.9257 (p0) cc_final: 0.8997 (p0) REVERT: C 233 PHE cc_start: 0.9200 (t80) cc_final: 0.8902 (t80) REVERT: C 251 ILE cc_start: 0.9153 (mt) cc_final: 0.8793 (mm) REVERT: C 300 ASN cc_start: 0.8930 (m-40) cc_final: 0.7874 (p0) REVERT: C 342 LEU cc_start: 0.9628 (mt) cc_final: 0.9342 (mm) REVERT: C 423 ILE cc_start: 0.9534 (mt) cc_final: 0.9267 (mt) REVERT: D 536 THR cc_start: 0.8298 (p) cc_final: 0.7769 (t) REVERT: D 540 GLN cc_start: 0.9228 (mp-120) cc_final: 0.8890 (mp10) REVERT: D 543 ASN cc_start: 0.8388 (m-40) cc_final: 0.7782 (t0) REVERT: D 614 TRP cc_start: 0.8207 (m-10) cc_final: 0.7734 (m-10) REVERT: D 615 SER cc_start: 0.9012 (t) cc_final: 0.8630 (m) REVERT: D 617 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.7205 (mmm-85) REVERT: E 51 THR cc_start: 0.9040 (m) cc_final: 0.8689 (p) REVERT: E 180 ASP cc_start: 0.9083 (m-30) cc_final: 0.8811 (m-30) REVERT: E 195 ASN cc_start: 0.9224 (p0) cc_final: 0.9006 (p0) REVERT: E 233 PHE cc_start: 0.9110 (t80) cc_final: 0.8641 (t80) REVERT: E 256 SER cc_start: 0.8245 (p) cc_final: 0.7784 (p) REVERT: E 300 ASN cc_start: 0.8959 (m-40) cc_final: 0.8691 (m-40) REVERT: E 342 LEU cc_start: 0.9625 (mt) cc_final: 0.9420 (mm) REVERT: F 530 MET cc_start: 0.8869 (mtp) cc_final: 0.8473 (mtp) REVERT: F 536 THR cc_start: 0.8654 (p) cc_final: 0.8041 (t) REVERT: F 540 GLN cc_start: 0.9253 (mp-120) cc_final: 0.8871 (mp10) REVERT: F 543 ASN cc_start: 0.8447 (m-40) cc_final: 0.8157 (t0) REVERT: F 615 SER cc_start: 0.8697 (t) cc_final: 0.8389 (m) REVERT: F 617 ARG cc_start: 0.7583 (ttm-80) cc_final: 0.7116 (mmm-85) REVERT: F 643 TYR cc_start: 0.8769 (m-10) cc_final: 0.8232 (m-10) outliers start: 3 outliers final: 3 residues processed: 459 average time/residue: 0.1131 time to fit residues: 77.0356 Evaluate side-chains 266 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 263 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 188 ASN A 422 GLN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 188 ASN C 422 GLN D 630 GLN E 185 ASN E 188 ASN E 422 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.106769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.082722 restraints weight = 30234.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.085542 restraints weight = 18749.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.087504 restraints weight = 13817.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.088810 restraints weight = 11331.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.089549 restraints weight = 9941.981| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15336 Z= 0.234 Angle : 0.821 9.145 21009 Z= 0.402 Chirality : 0.048 0.223 2628 Planarity : 0.005 0.058 2484 Dihedral : 9.383 79.183 3933 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.52 % Allowed : 2.23 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.20), residues: 1674 helix: 1.40 (0.26), residues: 393 sheet: 1.40 (0.24), residues: 411 loop : 0.45 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 617 TYR 0.018 0.002 TYR D 643 PHE 0.014 0.002 PHE C 176 TRP 0.037 0.002 TRP A 479 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00522 (15201) covalent geometry : angle 0.74973 (20637) SS BOND : bond 0.00507 ( 33) SS BOND : angle 1.82096 ( 66) hydrogen bonds : bond 0.06032 ( 555) hydrogen bonds : angle 5.59828 ( 1791) link_ALPHA1-3 : bond 0.00879 ( 3) link_ALPHA1-3 : angle 3.93540 ( 9) link_ALPHA1-6 : bond 0.00868 ( 3) link_ALPHA1-6 : angle 2.04661 ( 9) link_BETA1-4 : bond 0.00559 ( 33) link_BETA1-4 : angle 1.96795 ( 99) link_NAG-ASN : bond 0.00487 ( 63) link_NAG-ASN : angle 3.07277 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 330 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8995 (m) cc_final: 0.8472 (p) REVERT: A 180 ASP cc_start: 0.9123 (m-30) cc_final: 0.8860 (m-30) REVERT: A 217 TYR cc_start: 0.8927 (m-80) cc_final: 0.8425 (m-80) REVERT: A 256 SER cc_start: 0.8225 (p) cc_final: 0.7917 (p) REVERT: B 536 THR cc_start: 0.8587 (p) cc_final: 0.8145 (t) REVERT: B 542 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.7237 (ttm-80) REVERT: B 543 ASN cc_start: 0.8372 (m-40) cc_final: 0.7944 (t0) REVERT: B 615 SER cc_start: 0.8659 (t) cc_final: 0.8188 (m) REVERT: B 638 TYR cc_start: 0.8637 (m-80) cc_final: 0.8374 (m-10) REVERT: B 656 ASN cc_start: 0.8723 (m-40) cc_final: 0.8391 (m110) REVERT: C 87 GLU cc_start: 0.8361 (tt0) cc_final: 0.8118 (tp30) REVERT: C 114 GLN cc_start: 0.8494 (tp40) cc_final: 0.8283 (tp40) REVERT: C 256 SER cc_start: 0.8242 (p) cc_final: 0.7895 (p) REVERT: C 300 ASN cc_start: 0.8092 (m-40) cc_final: 0.7744 (m-40) REVERT: C 356 ASN cc_start: 0.8398 (p0) cc_final: 0.8191 (p0) REVERT: C 479 TRP cc_start: 0.8472 (m-10) cc_final: 0.7944 (m-10) REVERT: D 536 THR cc_start: 0.8406 (p) cc_final: 0.8101 (t) REVERT: D 543 ASN cc_start: 0.8415 (m-40) cc_final: 0.7896 (t0) REVERT: D 614 TRP cc_start: 0.8315 (m-10) cc_final: 0.7750 (m-10) REVERT: D 615 SER cc_start: 0.8584 (t) cc_final: 0.8281 (m) REVERT: D 632 ASP cc_start: 0.9114 (t70) cc_final: 0.8846 (t0) REVERT: D 638 TYR cc_start: 0.8469 (m-80) cc_final: 0.8100 (m-10) REVERT: E 51 THR cc_start: 0.9103 (m) cc_final: 0.8696 (p) REVERT: E 180 ASP cc_start: 0.9170 (m-30) cc_final: 0.8830 (m-30) REVERT: E 256 SER cc_start: 0.8290 (p) cc_final: 0.8008 (p) REVERT: E 479 TRP cc_start: 0.8447 (m-10) cc_final: 0.8085 (m-10) REVERT: F 536 THR cc_start: 0.8482 (p) cc_final: 0.8221 (t) REVERT: F 543 ASN cc_start: 0.8450 (m-40) cc_final: 0.8175 (t0) REVERT: F 615 SER cc_start: 0.8580 (t) cc_final: 0.8292 (m) REVERT: F 617 ARG cc_start: 0.7892 (ttm-80) cc_final: 0.7690 (mmm-85) REVERT: F 618 ASN cc_start: 0.5329 (m110) cc_final: 0.5123 (m110) REVERT: F 621 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7796 (tm-30) REVERT: F 638 TYR cc_start: 0.8299 (m-80) cc_final: 0.7909 (m-10) outliers start: 8 outliers final: 0 residues processed: 335 average time/residue: 0.0961 time to fit residues: 50.3750 Evaluate side-chains 240 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 30 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 170 GLN A 216 HIS C 85 HIS C 170 GLN C 216 HIS E 85 HIS E 170 GLN E 216 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.079818 restraints weight = 30610.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.082470 restraints weight = 18948.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.084300 restraints weight = 14001.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.085410 restraints weight = 11500.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.086264 restraints weight = 10150.170| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 15336 Z= 0.265 Angle : 0.788 12.769 21009 Z= 0.390 Chirality : 0.048 0.332 2628 Planarity : 0.005 0.054 2484 Dihedral : 8.931 77.637 3933 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.33 % Allowed : 2.62 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1674 helix: 1.41 (0.27), residues: 402 sheet: 1.01 (0.23), residues: 453 loop : 0.10 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 542 TYR 0.017 0.002 TYR B 643 PHE 0.013 0.002 PHE E 176 TRP 0.043 0.002 TRP A 479 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00609 (15201) covalent geometry : angle 0.72443 (20637) SS BOND : bond 0.00433 ( 33) SS BOND : angle 2.31450 ( 66) hydrogen bonds : bond 0.05668 ( 555) hydrogen bonds : angle 5.28033 ( 1791) link_ALPHA1-3 : bond 0.01150 ( 3) link_ALPHA1-3 : angle 2.97132 ( 9) link_ALPHA1-6 : bond 0.00461 ( 3) link_ALPHA1-6 : angle 2.10084 ( 9) link_BETA1-4 : bond 0.00316 ( 33) link_BETA1-4 : angle 1.63382 ( 99) link_NAG-ASN : bond 0.00420 ( 63) link_NAG-ASN : angle 2.80999 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 278 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9218 (m) cc_final: 0.8871 (p) REVERT: A 180 ASP cc_start: 0.9140 (m-30) cc_final: 0.8833 (m-30) REVERT: A 256 SER cc_start: 0.8343 (p) cc_final: 0.8095 (p) REVERT: A 342 LEU cc_start: 0.9403 (mm) cc_final: 0.8757 (tp) REVERT: A 423 ILE cc_start: 0.9494 (mt) cc_final: 0.9260 (mm) REVERT: B 536 THR cc_start: 0.8793 (p) cc_final: 0.7851 (t) REVERT: B 540 GLN cc_start: 0.9208 (mp-120) cc_final: 0.8666 (mp10) REVERT: B 615 SER cc_start: 0.8975 (t) cc_final: 0.8475 (m) REVERT: B 656 ASN cc_start: 0.8700 (m-40) cc_final: 0.8487 (m-40) REVERT: C 256 SER cc_start: 0.8603 (p) cc_final: 0.8234 (p) REVERT: C 342 LEU cc_start: 0.9406 (mm) cc_final: 0.8738 (tp) REVERT: D 543 ASN cc_start: 0.8501 (m-40) cc_final: 0.7821 (t0) REVERT: D 614 TRP cc_start: 0.8507 (m-10) cc_final: 0.7554 (m-10) REVERT: D 615 SER cc_start: 0.8741 (t) cc_final: 0.8344 (m) REVERT: D 638 TYR cc_start: 0.8358 (m-80) cc_final: 0.7982 (m-10) REVERT: D 642 ILE cc_start: 0.9581 (mm) cc_final: 0.9264 (mm) REVERT: E 51 THR cc_start: 0.9213 (m) cc_final: 0.8817 (p) REVERT: E 180 ASP cc_start: 0.9180 (m-30) cc_final: 0.8841 (m-30) REVERT: E 256 SER cc_start: 0.8547 (p) cc_final: 0.8216 (p) REVERT: E 342 LEU cc_start: 0.9424 (mm) cc_final: 0.8750 (tp) REVERT: E 423 ILE cc_start: 0.9500 (mt) cc_final: 0.9216 (mm) REVERT: F 535 MET cc_start: 0.8816 (mmt) cc_final: 0.8525 (mmt) REVERT: F 536 THR cc_start: 0.8744 (p) cc_final: 0.8408 (t) REVERT: F 543 ASN cc_start: 0.8635 (m-40) cc_final: 0.7982 (t0) REVERT: F 615 SER cc_start: 0.8732 (t) cc_final: 0.8379 (m) REVERT: F 618 ASN cc_start: 0.5441 (m110) cc_final: 0.5195 (m110) REVERT: F 621 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7996 (tm-30) REVERT: F 632 ASP cc_start: 0.9237 (t0) cc_final: 0.8912 (t0) REVERT: F 638 TYR cc_start: 0.8303 (m-80) cc_final: 0.7899 (m-10) outliers start: 5 outliers final: 2 residues processed: 281 average time/residue: 0.0924 time to fit residues: 41.2785 Evaluate side-chains 219 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 91 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 152 optimal weight: 30.0000 chunk 20 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 164 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.105002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.080902 restraints weight = 30103.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.083790 restraints weight = 18108.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.085776 restraints weight = 13116.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.087081 restraints weight = 10636.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.087927 restraints weight = 9285.133| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15336 Z= 0.154 Angle : 0.693 12.527 21009 Z= 0.342 Chirality : 0.047 0.314 2628 Planarity : 0.004 0.057 2484 Dihedral : 8.181 72.398 3933 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.20 % Allowed : 1.71 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.20), residues: 1674 helix: 1.72 (0.27), residues: 393 sheet: 0.98 (0.23), residues: 453 loop : 0.04 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 617 TYR 0.024 0.001 TYR B 638 PHE 0.011 0.001 PHE C 176 TRP 0.034 0.002 TRP A 479 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00347 (15201) covalent geometry : angle 0.63054 (20637) SS BOND : bond 0.00475 ( 33) SS BOND : angle 2.60311 ( 66) hydrogen bonds : bond 0.04808 ( 555) hydrogen bonds : angle 4.95925 ( 1791) link_ALPHA1-3 : bond 0.00975 ( 3) link_ALPHA1-3 : angle 2.62295 ( 9) link_ALPHA1-6 : bond 0.00862 ( 3) link_ALPHA1-6 : angle 2.18720 ( 9) link_BETA1-4 : bond 0.00400 ( 33) link_BETA1-4 : angle 1.30599 ( 99) link_NAG-ASN : bond 0.00256 ( 63) link_NAG-ASN : angle 2.48841 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 259 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9194 (m) cc_final: 0.8738 (p) REVERT: A 180 ASP cc_start: 0.9145 (m-30) cc_final: 0.8928 (m-30) REVERT: A 256 SER cc_start: 0.8266 (p) cc_final: 0.7995 (p) REVERT: B 536 THR cc_start: 0.8725 (p) cc_final: 0.8418 (t) REVERT: B 615 SER cc_start: 0.8857 (t) cc_final: 0.8418 (m) REVERT: B 631 TRP cc_start: 0.9083 (t-100) cc_final: 0.8829 (t-100) REVERT: C 51 THR cc_start: 0.9196 (m) cc_final: 0.8829 (p) REVERT: C 256 SER cc_start: 0.8625 (p) cc_final: 0.8291 (p) REVERT: C 342 LEU cc_start: 0.9300 (mm) cc_final: 0.8678 (tp) REVERT: D 543 ASN cc_start: 0.8575 (m-40) cc_final: 0.7824 (t0) REVERT: D 614 TRP cc_start: 0.8526 (m-10) cc_final: 0.7471 (m-10) REVERT: D 615 SER cc_start: 0.8663 (t) cc_final: 0.8154 (m) REVERT: D 638 TYR cc_start: 0.8285 (m-80) cc_final: 0.7868 (m-10) REVERT: D 642 ILE cc_start: 0.9587 (mm) cc_final: 0.9318 (mm) REVERT: E 51 THR cc_start: 0.9321 (m) cc_final: 0.8903 (p) REVERT: E 114 GLN cc_start: 0.8647 (tp40) cc_final: 0.8273 (tp40) REVERT: E 180 ASP cc_start: 0.9185 (m-30) cc_final: 0.8886 (m-30) REVERT: E 256 SER cc_start: 0.8530 (p) cc_final: 0.8248 (p) REVERT: E 342 LEU cc_start: 0.9305 (mm) cc_final: 0.8676 (tp) REVERT: E 423 ILE cc_start: 0.9488 (mt) cc_final: 0.9260 (mm) REVERT: F 536 THR cc_start: 0.8693 (p) cc_final: 0.8471 (t) REVERT: F 543 ASN cc_start: 0.8532 (m-40) cc_final: 0.8080 (t0) REVERT: F 615 SER cc_start: 0.8758 (t) cc_final: 0.8483 (m) REVERT: F 617 ARG cc_start: 0.7958 (mtp180) cc_final: 0.7334 (mmm-85) REVERT: F 621 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8206 (tm-30) REVERT: F 626 MET cc_start: 0.8561 (mmm) cc_final: 0.8327 (mmm) REVERT: F 632 ASP cc_start: 0.9183 (t0) cc_final: 0.8891 (t0) REVERT: F 638 TYR cc_start: 0.8164 (m-80) cc_final: 0.7671 (m-10) outliers start: 3 outliers final: 2 residues processed: 261 average time/residue: 0.0915 time to fit residues: 38.4773 Evaluate side-chains 221 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 219 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 128 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 570 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 HIS ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.078205 restraints weight = 30312.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.080935 restraints weight = 18471.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.082787 restraints weight = 13502.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.083939 restraints weight = 11047.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.084841 restraints weight = 9733.115| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15336 Z= 0.237 Angle : 0.745 11.547 21009 Z= 0.369 Chirality : 0.048 0.280 2628 Planarity : 0.004 0.055 2484 Dihedral : 8.096 67.275 3933 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 1674 helix: 1.43 (0.27), residues: 411 sheet: 1.51 (0.26), residues: 363 loop : -0.34 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 542 TYR 0.023 0.002 TYR A 486 PHE 0.011 0.001 PHE C 176 TRP 0.062 0.002 TRP A 479 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00547 (15201) covalent geometry : angle 0.68844 (20637) SS BOND : bond 0.00662 ( 33) SS BOND : angle 2.65752 ( 66) hydrogen bonds : bond 0.05122 ( 555) hydrogen bonds : angle 4.93126 ( 1791) link_ALPHA1-3 : bond 0.00929 ( 3) link_ALPHA1-3 : angle 2.91736 ( 9) link_ALPHA1-6 : bond 0.00904 ( 3) link_ALPHA1-6 : angle 2.51461 ( 9) link_BETA1-4 : bond 0.00269 ( 33) link_BETA1-4 : angle 1.39866 ( 99) link_NAG-ASN : bond 0.00414 ( 63) link_NAG-ASN : angle 2.41302 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9285 (m) cc_final: 0.8830 (p) REVERT: A 180 ASP cc_start: 0.9191 (m-30) cc_final: 0.8966 (m-30) REVERT: A 256 SER cc_start: 0.8453 (p) cc_final: 0.8100 (p) REVERT: B 530 MET cc_start: 0.8727 (mtp) cc_final: 0.8365 (mmm) REVERT: B 536 THR cc_start: 0.8778 (p) cc_final: 0.8559 (t) REVERT: B 615 SER cc_start: 0.8703 (t) cc_final: 0.8237 (m) REVERT: C 51 THR cc_start: 0.9302 (m) cc_final: 0.8987 (p) REVERT: C 114 GLN cc_start: 0.8682 (tp40) cc_final: 0.8368 (tp40) REVERT: C 217 TYR cc_start: 0.8989 (m-80) cc_final: 0.8785 (m-80) REVERT: C 256 SER cc_start: 0.8813 (p) cc_final: 0.8495 (p) REVERT: C 284 ILE cc_start: 0.9450 (mt) cc_final: 0.8971 (tt) REVERT: D 540 GLN cc_start: 0.9093 (mp-120) cc_final: 0.8699 (mp10) REVERT: D 614 TRP cc_start: 0.8624 (m-10) cc_final: 0.7657 (m-10) REVERT: D 615 SER cc_start: 0.8472 (t) cc_final: 0.7809 (m) REVERT: D 632 ASP cc_start: 0.9237 (t0) cc_final: 0.9024 (t0) REVERT: D 638 TYR cc_start: 0.8306 (m-80) cc_final: 0.7757 (m-10) REVERT: D 642 ILE cc_start: 0.9591 (mm) cc_final: 0.9314 (mm) REVERT: E 51 THR cc_start: 0.9400 (m) cc_final: 0.9052 (p) REVERT: E 180 ASP cc_start: 0.9207 (m-30) cc_final: 0.8685 (m-30) REVERT: E 256 SER cc_start: 0.8765 (p) cc_final: 0.8435 (p) REVERT: E 423 ILE cc_start: 0.9525 (mt) cc_final: 0.9057 (mt) REVERT: F 530 MET cc_start: 0.8679 (mtp) cc_final: 0.8293 (mtp) REVERT: F 535 MET cc_start: 0.8882 (mmp) cc_final: 0.8641 (mmt) REVERT: F 615 SER cc_start: 0.8775 (t) cc_final: 0.8211 (m) REVERT: F 621 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8222 (tm-30) REVERT: F 632 ASP cc_start: 0.9226 (t0) cc_final: 0.8916 (t0) REVERT: F 638 TYR cc_start: 0.8191 (m-80) cc_final: 0.7748 (m-10) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.0916 time to fit residues: 36.1411 Evaluate side-chains 208 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 66 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 66 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.100626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.076442 restraints weight = 30677.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.079054 restraints weight = 19137.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.080848 restraints weight = 14217.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.081944 restraints weight = 11743.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.082759 restraints weight = 10424.973| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 15336 Z= 0.279 Angle : 0.794 13.266 21009 Z= 0.391 Chirality : 0.049 0.301 2628 Planarity : 0.005 0.127 2484 Dihedral : 8.075 62.605 3933 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.20), residues: 1674 helix: 1.09 (0.26), residues: 411 sheet: 1.12 (0.26), residues: 396 loop : -0.54 (0.19), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 542 TYR 0.015 0.002 TYR B 638 PHE 0.012 0.002 PHE C 376 TRP 0.049 0.002 TRP E 479 HIS 0.006 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00646 (15201) covalent geometry : angle 0.74099 (20637) SS BOND : bond 0.00790 ( 33) SS BOND : angle 2.73927 ( 66) hydrogen bonds : bond 0.05367 ( 555) hydrogen bonds : angle 5.01647 ( 1791) link_ALPHA1-3 : bond 0.00949 ( 3) link_ALPHA1-3 : angle 3.20486 ( 9) link_ALPHA1-6 : bond 0.00878 ( 3) link_ALPHA1-6 : angle 2.62121 ( 9) link_BETA1-4 : bond 0.00307 ( 33) link_BETA1-4 : angle 1.39517 ( 99) link_NAG-ASN : bond 0.00393 ( 63) link_NAG-ASN : angle 2.39145 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 SER cc_start: 0.8591 (p) cc_final: 0.8224 (p) REVERT: B 530 MET cc_start: 0.8800 (mtp) cc_final: 0.8510 (mtp) REVERT: B 638 TYR cc_start: 0.8614 (m-80) cc_final: 0.8121 (m-10) REVERT: C 256 SER cc_start: 0.8865 (p) cc_final: 0.8638 (p) REVERT: C 284 ILE cc_start: 0.9502 (mt) cc_final: 0.9054 (tt) REVERT: C 486 TYR cc_start: 0.8773 (m-80) cc_final: 0.8549 (m-10) REVERT: D 601 LYS cc_start: 0.8727 (mptt) cc_final: 0.8499 (mmtm) REVERT: D 615 SER cc_start: 0.8605 (t) cc_final: 0.7848 (m) REVERT: D 632 ASP cc_start: 0.9244 (t0) cc_final: 0.8967 (t0) REVERT: D 638 TYR cc_start: 0.8427 (m-80) cc_final: 0.7971 (m-10) REVERT: E 51 THR cc_start: 0.9378 (m) cc_final: 0.8967 (p) REVERT: E 114 GLN cc_start: 0.8810 (tp40) cc_final: 0.8479 (tp40) REVERT: E 180 ASP cc_start: 0.9225 (m-30) cc_final: 0.8827 (m-30) REVERT: E 210 PHE cc_start: 0.9044 (m-80) cc_final: 0.8434 (m-80) REVERT: E 256 SER cc_start: 0.8807 (p) cc_final: 0.8535 (p) REVERT: E 423 ILE cc_start: 0.9573 (mt) cc_final: 0.9263 (mm) REVERT: F 530 MET cc_start: 0.8704 (mtp) cc_final: 0.8411 (mtp) REVERT: F 535 MET cc_start: 0.8999 (mmp) cc_final: 0.8717 (mmt) REVERT: F 540 GLN cc_start: 0.9157 (mp-120) cc_final: 0.8774 (mp10) REVERT: F 542 ARG cc_start: 0.8241 (mtm180) cc_final: 0.7782 (mtm-85) REVERT: F 584 GLU cc_start: 0.8655 (tt0) cc_final: 0.8367 (tt0) REVERT: F 615 SER cc_start: 0.8785 (t) cc_final: 0.8203 (m) REVERT: F 621 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8216 (tm-30) REVERT: F 626 MET cc_start: 0.8191 (mmm) cc_final: 0.7920 (mmm) REVERT: F 632 ASP cc_start: 0.9199 (t0) cc_final: 0.8943 (t0) REVERT: F 638 TYR cc_start: 0.8404 (m-80) cc_final: 0.7769 (m-10) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.0899 time to fit residues: 33.2352 Evaluate side-chains 189 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 112 optimal weight: 0.0980 chunk 110 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 656 ASN B 658 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.081159 restraints weight = 29745.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.083968 restraints weight = 17994.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.085934 restraints weight = 13086.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.087200 restraints weight = 10606.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.088028 restraints weight = 9275.280| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15336 Z= 0.118 Angle : 0.656 12.398 21009 Z= 0.327 Chirality : 0.046 0.266 2628 Planarity : 0.004 0.050 2484 Dihedral : 7.348 57.409 3933 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.07 % Allowed : 1.57 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.20), residues: 1674 helix: 1.47 (0.27), residues: 393 sheet: 0.93 (0.25), residues: 405 loop : -0.25 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 542 TYR 0.014 0.001 TYR C 217 PHE 0.008 0.001 PHE E 383 TRP 0.035 0.001 TRP E 479 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00255 (15201) covalent geometry : angle 0.60645 (20637) SS BOND : bond 0.00459 ( 33) SS BOND : angle 2.44105 ( 66) hydrogen bonds : bond 0.04491 ( 555) hydrogen bonds : angle 4.75669 ( 1791) link_ALPHA1-3 : bond 0.01269 ( 3) link_ALPHA1-3 : angle 2.50191 ( 9) link_ALPHA1-6 : bond 0.00988 ( 3) link_ALPHA1-6 : angle 2.05624 ( 9) link_BETA1-4 : bond 0.00422 ( 33) link_BETA1-4 : angle 1.06991 ( 99) link_NAG-ASN : bond 0.00180 ( 63) link_NAG-ASN : angle 2.11810 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9408 (tpp) cc_final: 0.9183 (tpt) REVERT: A 256 SER cc_start: 0.8323 (p) cc_final: 0.8021 (p) REVERT: B 530 MET cc_start: 0.8556 (mtp) cc_final: 0.8218 (mmm) REVERT: B 638 TYR cc_start: 0.8268 (m-80) cc_final: 0.8054 (m-10) REVERT: C 51 THR cc_start: 0.9256 (m) cc_final: 0.8943 (p) REVERT: C 247 CYS cc_start: 0.5352 (p) cc_final: 0.4968 (p) REVERT: C 256 SER cc_start: 0.8586 (p) cc_final: 0.8209 (p) REVERT: C 284 ILE cc_start: 0.9468 (mt) cc_final: 0.9076 (tt) REVERT: D 601 LYS cc_start: 0.8665 (mptt) cc_final: 0.8438 (mmtm) REVERT: D 614 TRP cc_start: 0.8680 (m-10) cc_final: 0.7562 (m-10) REVERT: D 615 SER cc_start: 0.8411 (t) cc_final: 0.7925 (m) REVERT: D 632 ASP cc_start: 0.9160 (t0) cc_final: 0.8942 (t0) REVERT: D 638 TYR cc_start: 0.8180 (m-80) cc_final: 0.7677 (m-10) REVERT: D 642 ILE cc_start: 0.9465 (mm) cc_final: 0.9219 (mm) REVERT: E 51 THR cc_start: 0.9381 (m) cc_final: 0.9101 (p) REVERT: E 180 ASP cc_start: 0.9145 (m-30) cc_final: 0.8725 (m-30) REVERT: E 195 ASN cc_start: 0.8584 (p0) cc_final: 0.8333 (p0) REVERT: E 210 PHE cc_start: 0.9013 (m-80) cc_final: 0.8420 (m-80) REVERT: E 247 CYS cc_start: 0.5057 (p) cc_final: 0.4727 (p) REVERT: E 256 SER cc_start: 0.8700 (p) cc_final: 0.8336 (p) REVERT: E 342 LEU cc_start: 0.9174 (mm) cc_final: 0.8657 (tp) REVERT: E 423 ILE cc_start: 0.9524 (mt) cc_final: 0.9223 (mt) REVERT: E 439 ILE cc_start: 0.9403 (mm) cc_final: 0.9168 (mm) REVERT: F 530 MET cc_start: 0.8374 (mtp) cc_final: 0.7760 (mmm) REVERT: F 535 MET cc_start: 0.8901 (mmp) cc_final: 0.8610 (mmt) REVERT: F 540 GLN cc_start: 0.9085 (mp-120) cc_final: 0.8663 (mp10) REVERT: F 542 ARG cc_start: 0.8253 (mtm180) cc_final: 0.7711 (mtm-85) REVERT: F 584 GLU cc_start: 0.8517 (tt0) cc_final: 0.8160 (tt0) REVERT: F 615 SER cc_start: 0.8672 (t) cc_final: 0.8073 (m) REVERT: F 621 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8304 (tm-30) REVERT: F 632 ASP cc_start: 0.9127 (t0) cc_final: 0.8882 (t0) REVERT: F 638 TYR cc_start: 0.8152 (m-80) cc_final: 0.7573 (m-10) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.0922 time to fit residues: 36.6800 Evaluate side-chains 205 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN C 85 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN E 85 HIS ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.078660 restraints weight = 30333.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.081368 restraints weight = 18471.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.083237 restraints weight = 13502.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.084475 restraints weight = 11013.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.085227 restraints weight = 9640.698| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15336 Z= 0.208 Angle : 0.730 11.956 21009 Z= 0.361 Chirality : 0.048 0.287 2628 Planarity : 0.004 0.055 2484 Dihedral : 7.212 58.100 3933 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.20), residues: 1674 helix: 1.40 (0.27), residues: 396 sheet: 0.85 (0.25), residues: 402 loop : -0.39 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 503 TYR 0.014 0.001 TYR B 638 PHE 0.009 0.001 PHE C 376 TRP 0.057 0.002 TRP E 479 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00483 (15201) covalent geometry : angle 0.67971 (20637) SS BOND : bond 0.00519 ( 33) SS BOND : angle 2.73698 ( 66) hydrogen bonds : bond 0.04814 ( 555) hydrogen bonds : angle 4.84674 ( 1791) link_ALPHA1-3 : bond 0.01031 ( 3) link_ALPHA1-3 : angle 2.94301 ( 9) link_ALPHA1-6 : bond 0.00796 ( 3) link_ALPHA1-6 : angle 2.14223 ( 9) link_BETA1-4 : bond 0.00315 ( 33) link_BETA1-4 : angle 1.26858 ( 99) link_NAG-ASN : bond 0.00301 ( 63) link_NAG-ASN : angle 2.18054 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9205 (tpp) cc_final: 0.8835 (tpt) REVERT: A 256 SER cc_start: 0.8422 (p) cc_final: 0.8035 (p) REVERT: B 530 MET cc_start: 0.8634 (mtp) cc_final: 0.8297 (mmm) REVERT: B 631 TRP cc_start: 0.9143 (t-100) cc_final: 0.8753 (t-100) REVERT: B 654 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7826 (mp0) REVERT: C 256 SER cc_start: 0.8706 (p) cc_final: 0.8419 (p) REVERT: C 284 ILE cc_start: 0.9556 (mt) cc_final: 0.9222 (tt) REVERT: D 530 MET cc_start: 0.9067 (mmm) cc_final: 0.8788 (mmt) REVERT: D 615 SER cc_start: 0.8564 (t) cc_final: 0.7852 (m) REVERT: D 632 ASP cc_start: 0.9212 (t0) cc_final: 0.8932 (t0) REVERT: D 638 TYR cc_start: 0.8269 (m-80) cc_final: 0.7822 (m-10) REVERT: E 51 THR cc_start: 0.9397 (m) cc_final: 0.9018 (p) REVERT: E 104 MET cc_start: 0.8821 (tpp) cc_final: 0.8568 (tpp) REVERT: E 114 GLN cc_start: 0.8657 (tp40) cc_final: 0.8375 (tp40) REVERT: E 161 MET cc_start: 0.8779 (tpp) cc_final: 0.8361 (tpp) REVERT: E 180 ASP cc_start: 0.9195 (m-30) cc_final: 0.8817 (m-30) REVERT: E 195 ASN cc_start: 0.8749 (p0) cc_final: 0.8548 (p0) REVERT: E 210 PHE cc_start: 0.9044 (m-80) cc_final: 0.8434 (m-80) REVERT: E 256 SER cc_start: 0.8818 (p) cc_final: 0.8508 (p) REVERT: E 423 ILE cc_start: 0.9553 (mt) cc_final: 0.9306 (mm) REVERT: F 530 MET cc_start: 0.8531 (mtp) cc_final: 0.8042 (mtp) REVERT: F 535 MET cc_start: 0.8949 (mmp) cc_final: 0.8659 (mmt) REVERT: F 542 ARG cc_start: 0.8360 (mtm180) cc_final: 0.8085 (ttm-80) REVERT: F 584 GLU cc_start: 0.8470 (tt0) cc_final: 0.7969 (tt0) REVERT: F 615 SER cc_start: 0.8540 (t) cc_final: 0.7877 (m) REVERT: F 621 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8150 (tm-30) REVERT: F 638 TYR cc_start: 0.8290 (m-80) cc_final: 0.7602 (m-10) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.0873 time to fit residues: 31.2613 Evaluate side-chains 181 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 158 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 120 optimal weight: 0.0970 chunk 22 optimal weight: 5.9990 chunk 106 optimal weight: 0.0980 chunk 128 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.107255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.083732 restraints weight = 29798.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.086606 restraints weight = 17964.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.088581 restraints weight = 12998.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.089899 restraints weight = 10512.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.090706 restraints weight = 9142.020| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15336 Z= 0.115 Angle : 0.641 11.161 21009 Z= 0.322 Chirality : 0.046 0.235 2628 Planarity : 0.004 0.057 2484 Dihedral : 5.903 53.088 3933 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 1674 helix: 1.38 (0.26), residues: 396 sheet: 0.93 (0.25), residues: 405 loop : -0.30 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 542 TYR 0.042 0.001 TYR B 638 PHE 0.008 0.001 PHE A 383 TRP 0.045 0.001 TRP E 479 HIS 0.007 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00238 (15201) covalent geometry : angle 0.59390 (20637) SS BOND : bond 0.00699 ( 33) SS BOND : angle 2.44610 ( 66) hydrogen bonds : bond 0.04069 ( 555) hydrogen bonds : angle 4.64783 ( 1791) link_ALPHA1-3 : bond 0.01176 ( 3) link_ALPHA1-3 : angle 2.03061 ( 9) link_ALPHA1-6 : bond 0.00585 ( 3) link_ALPHA1-6 : angle 1.79897 ( 9) link_BETA1-4 : bond 0.00475 ( 33) link_BETA1-4 : angle 0.98556 ( 99) link_NAG-ASN : bond 0.00241 ( 63) link_NAG-ASN : angle 2.06435 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.7625 (m-90) cc_final: 0.7419 (m100) REVERT: A 161 MET cc_start: 0.9237 (tpp) cc_final: 0.8830 (tpt) REVERT: A 180 ASP cc_start: 0.9094 (m-30) cc_final: 0.8452 (m-30) REVERT: A 256 SER cc_start: 0.7962 (p) cc_final: 0.7661 (p) REVERT: A 423 ILE cc_start: 0.9496 (mt) cc_final: 0.9288 (mt) REVERT: B 608 VAL cc_start: 0.8806 (t) cc_final: 0.8594 (t) REVERT: B 614 TRP cc_start: 0.8369 (m-10) cc_final: 0.7657 (m-90) REVERT: B 631 TRP cc_start: 0.9121 (t-100) cc_final: 0.8915 (t-100) REVERT: B 642 ILE cc_start: 0.9517 (mm) cc_final: 0.9235 (mm) REVERT: C 51 THR cc_start: 0.9162 (m) cc_final: 0.8937 (p) REVERT: C 217 TYR cc_start: 0.8665 (m-80) cc_final: 0.8420 (m-80) REVERT: C 256 SER cc_start: 0.8646 (p) cc_final: 0.8363 (p) REVERT: C 284 ILE cc_start: 0.9489 (mt) cc_final: 0.9182 (tt) REVERT: D 530 MET cc_start: 0.9232 (mmm) cc_final: 0.8747 (mmt) REVERT: D 615 SER cc_start: 0.8364 (t) cc_final: 0.7668 (m) REVERT: D 632 ASP cc_start: 0.9181 (t0) cc_final: 0.8977 (t0) REVERT: D 638 TYR cc_start: 0.8116 (m-80) cc_final: 0.7669 (m-10) REVERT: E 51 THR cc_start: 0.9407 (m) cc_final: 0.9135 (p) REVERT: E 114 GLN cc_start: 0.8507 (tp40) cc_final: 0.8240 (tp40) REVERT: E 161 MET cc_start: 0.8869 (tpp) cc_final: 0.8451 (tpt) REVERT: E 210 PHE cc_start: 0.9041 (m-80) cc_final: 0.8498 (m-80) REVERT: E 256 SER cc_start: 0.8683 (p) cc_final: 0.8337 (p) REVERT: E 342 LEU cc_start: 0.9045 (mm) cc_final: 0.8570 (tp) REVERT: F 530 MET cc_start: 0.8396 (mtp) cc_final: 0.7849 (mmm) REVERT: F 535 MET cc_start: 0.8911 (mmp) cc_final: 0.8600 (mmt) REVERT: F 538 THR cc_start: 0.8929 (p) cc_final: 0.8682 (t) REVERT: F 584 GLU cc_start: 0.8378 (tt0) cc_final: 0.7932 (tt0) REVERT: F 603 ILE cc_start: 0.9457 (mp) cc_final: 0.9210 (mm) REVERT: F 615 SER cc_start: 0.8561 (t) cc_final: 0.7880 (m) REVERT: F 626 MET cc_start: 0.7890 (mmm) cc_final: 0.7393 (mmm) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.0828 time to fit residues: 33.1341 Evaluate side-chains 213 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 160 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 117 optimal weight: 0.0980 chunk 161 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 656 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.081392 restraints weight = 30389.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.084131 restraints weight = 18528.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.086034 restraints weight = 13614.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.087285 restraints weight = 11124.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.088076 restraints weight = 9753.630| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15336 Z= 0.143 Angle : 0.642 11.772 21009 Z= 0.323 Chirality : 0.045 0.249 2628 Planarity : 0.004 0.052 2484 Dihedral : 5.662 55.476 3933 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1674 helix: 1.37 (0.27), residues: 396 sheet: 0.78 (0.25), residues: 411 loop : -0.24 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 178 TYR 0.019 0.001 TYR B 638 PHE 0.007 0.001 PHE C 376 TRP 0.055 0.002 TRP A 479 HIS 0.003 0.001 HIS F 570 Details of bonding type rmsd covalent geometry : bond 0.00328 (15201) covalent geometry : angle 0.59429 (20637) SS BOND : bond 0.00388 ( 33) SS BOND : angle 2.47694 ( 66) hydrogen bonds : bond 0.04239 ( 555) hydrogen bonds : angle 4.66914 ( 1791) link_ALPHA1-3 : bond 0.00963 ( 3) link_ALPHA1-3 : angle 2.10812 ( 9) link_ALPHA1-6 : bond 0.00147 ( 3) link_ALPHA1-6 : angle 1.60567 ( 9) link_BETA1-4 : bond 0.00359 ( 33) link_BETA1-4 : angle 1.12682 ( 99) link_NAG-ASN : bond 0.00199 ( 63) link_NAG-ASN : angle 2.02733 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9214 (tpp) cc_final: 0.8793 (tpt) REVERT: A 180 ASP cc_start: 0.9146 (m-30) cc_final: 0.8482 (m-30) REVERT: A 256 SER cc_start: 0.8120 (p) cc_final: 0.7762 (p) REVERT: A 284 ILE cc_start: 0.9470 (mt) cc_final: 0.9191 (tt) REVERT: A 423 ILE cc_start: 0.9515 (mt) cc_final: 0.9299 (mt) REVERT: B 530 MET cc_start: 0.9289 (mmm) cc_final: 0.9056 (mmt) REVERT: B 608 VAL cc_start: 0.8804 (t) cc_final: 0.8593 (t) REVERT: B 614 TRP cc_start: 0.8302 (m-10) cc_final: 0.7633 (m-90) REVERT: B 642 ILE cc_start: 0.9481 (mm) cc_final: 0.9203 (mm) REVERT: C 51 THR cc_start: 0.9183 (m) cc_final: 0.8949 (p) REVERT: C 217 TYR cc_start: 0.8583 (m-80) cc_final: 0.8367 (m-80) REVERT: C 284 ILE cc_start: 0.9511 (mt) cc_final: 0.9243 (tt) REVERT: D 530 MET cc_start: 0.9222 (mmm) cc_final: 0.8742 (mmt) REVERT: D 615 SER cc_start: 0.8358 (t) cc_final: 0.7619 (m) REVERT: E 51 THR cc_start: 0.9335 (m) cc_final: 0.9048 (p) REVERT: E 161 MET cc_start: 0.8914 (tpp) cc_final: 0.8516 (tpp) REVERT: E 180 ASP cc_start: 0.9156 (m-30) cc_final: 0.8934 (m-30) REVERT: E 195 ASN cc_start: 0.8721 (p0) cc_final: 0.8302 (p0) REVERT: E 210 PHE cc_start: 0.9048 (m-80) cc_final: 0.8512 (m-80) REVERT: E 256 SER cc_start: 0.8770 (p) cc_final: 0.8480 (p) REVERT: E 423 ILE cc_start: 0.9559 (mt) cc_final: 0.9279 (mt) REVERT: F 530 MET cc_start: 0.8409 (mtp) cc_final: 0.7768 (mtp) REVERT: F 535 MET cc_start: 0.8975 (mmp) cc_final: 0.8583 (mmt) REVERT: F 584 GLU cc_start: 0.8441 (tt0) cc_final: 0.7918 (tt0) REVERT: F 615 SER cc_start: 0.8482 (t) cc_final: 0.7904 (m) REVERT: F 626 MET cc_start: 0.7851 (mmm) cc_final: 0.7567 (mmm) REVERT: F 631 TRP cc_start: 0.9175 (t-100) cc_final: 0.8906 (t-100) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.0914 time to fit residues: 35.1752 Evaluate side-chains 202 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 148 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 133 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.102448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.078736 restraints weight = 30173.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.081429 restraints weight = 18663.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.083226 restraints weight = 13702.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.084418 restraints weight = 11244.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.085121 restraints weight = 9901.104| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15336 Z= 0.223 Angle : 0.715 11.774 21009 Z= 0.358 Chirality : 0.047 0.253 2628 Planarity : 0.005 0.053 2484 Dihedral : 6.050 57.357 3933 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1674 helix: 1.33 (0.26), residues: 396 sheet: 0.65 (0.25), residues: 414 loop : -0.37 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 178 TYR 0.040 0.002 TYR B 638 PHE 0.010 0.001 PHE C 376 TRP 0.063 0.002 TRP E 479 HIS 0.006 0.001 HIS D 585 Details of bonding type rmsd covalent geometry : bond 0.00518 (15201) covalent geometry : angle 0.66769 (20637) SS BOND : bond 0.00454 ( 33) SS BOND : angle 2.68692 ( 66) hydrogen bonds : bond 0.04792 ( 555) hydrogen bonds : angle 4.75518 ( 1791) link_ALPHA1-3 : bond 0.00848 ( 3) link_ALPHA1-3 : angle 2.41730 ( 9) link_ALPHA1-6 : bond 0.00032 ( 3) link_ALPHA1-6 : angle 1.67929 ( 9) link_BETA1-4 : bond 0.00295 ( 33) link_BETA1-4 : angle 1.29244 ( 99) link_NAG-ASN : bond 0.00298 ( 63) link_NAG-ASN : angle 2.09628 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1878.81 seconds wall clock time: 33 minutes 33.33 seconds (2013.33 seconds total)